Literature DB >> 26045719

Repbase Update, a database of repetitive elements in eukaryotic genomes.

Weidong Bao1, Kenji K Kojima2, Oleksiy Kohany1.   

Abstract

Repbase Update (RU) is a database of representative repeat sequences in eukaryotic genomes. Since its first development as a database of human repetitive sequences in 1992, RU has been serving as a well-curated reference database fundamental for almost all eukaryotic genome sequence analyses. Here, we introduce recent updates of RU, focusing on technical issues concerning the submission and updating of Repbase entries and will give short examples of using RU data. RU sincerely invites a broader submission of repeat sequences from the research community.

Entities:  

Keywords:  Database; Repbase Reports; Repbase Update; RepbaseSubmitter; Transposable element

Year:  2015        PMID： 26045719      PMCID： PMC4455052          DOI： 10.1186/s13100-015-0041-9

Source DB:  PubMed          Journal:  Mob DNA


  29 in total

Review 1.  Repbase Update, a database of eukaryotic repetitive elements.

Authors:  J Jurka; V V Kapitonov; A Pavlicek; P Klonowski; O Kohany; J Walichiewicz
Journal:  Cytogenet Genome Res       Date:  2005       Impact factor: 1.636

2.  The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies.

Authors:  Yao-Wu Yuan; Susan R Wessler
Journal:  Proc Natl Acad Sci U S A       Date:  2011-04-25       Impact factor: 11.205

3.  Zisupton--a novel superfamily of DNA transposable elements recently active in fish.

Authors:  Astrid Böhne; Qingchun Zhou; Amandine Darras; Cornelia Schmidt; Manfred Schartl; Delphine Galiana-Arnoux; Jean-Nicolas Volff
Journal:  Mol Biol Evol       Date:  2011-08-27       Impact factor: 16.240

4.  Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells.

Authors:  Z Ivics; P B Hackett; R H Plasterk; Z Izsvák
Journal:  Cell       Date:  1997-11-14       Impact factor: 41.582

5.  The age of Alu subfamilies.

Authors:  V Kapitonov; J Jurka
Journal:  J Mol Evol       Date:  1996-01       Impact factor: 2.395

6.  Considering transposable element diversification in de novo annotation approaches.

Authors:  Timothée Flutre; Elodie Duprat; Catherine Feuillet; Hadi Quesneville
Journal:  PLoS One       Date:  2011-01-31       Impact factor: 3.240

7.  Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes.

Authors:  Alexander Suh; Gennady Churakov; Meganathan P Ramakodi; Roy N Platt; Jerzy Jurka; Kenji K Kojima; Juan Caballero; Arian F Smit; Kent A Vliet; Federico G Hoffmann; Jürgen Brosius; Richard E Green; Edward L Braun; David A Ray; Jürgen Schmitz
Journal:  Genome Biol Evol       Date:  2014-12-11       Impact factor: 3.416

8.  PASTEC: an automatic transposable element classification tool.

Authors:  Claire Hoede; Sandie Arnoux; Mark Moisset; Timothée Chaumier; Olivier Inizan; Véronique Jamilloux; Hadi Quesneville
Journal:  PLoS One       Date:  2014-05-02       Impact factor: 3.240

9.  Dfam: a database of repetitive DNA based on profile hidden Markov models.

Authors:  Travis J Wheeler; Jody Clements; Sean R Eddy; Robert Hubley; Thomas A Jones; Jerzy Jurka; Arian F A Smit; Robert D Finn
Journal:  Nucleic Acids Res       Date:  2012-11-30       Impact factor: 16.971

10.  LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons.

Authors:  Zhao Xu; Hao Wang
Journal:  Nucleic Acids Res       Date:  2007-05-07       Impact factor: 16.971
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  847 in total

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Authors:  Aren E Marshall; Michael V Roes; Daniel T Passos; Megan C DeWeerd; Andrea C Chaikovsky; Julien Sage; Christopher J Howlett; Frederick A Dick
Journal:  Mol Cell Biol       Date:  2019-07-29       Impact factor: 4.272

2.  Degradation of the Repetitive Genomic Landscape in a Close Relative of Caenorhabditis elegans.

Authors:  Gavin C Woodruff; Anastasia A Teterina
Journal:  Mol Biol Evol       Date:  2020-09-01       Impact factor: 16.240

3.  Heterochromatic histone modifications at transposons in Xenopus tropicalis embryos.

Authors:  Ila van Kruijsbergen; Saartje Hontelez; Dei M Elurbe; Simon J van Heeringen; Martijn A Huynen; Gert Jan C Veenstra
Journal:  Dev Biol       Date:  2016-09-14       Impact factor: 3.582

4.  Polymerase IV Plays a Crucial Role in Pollen Development in Capsella.

Authors:  Zhenxing Wang; Nicolas Butel; Juan Santos-González; Filipe Borges; Jun Yi; Robert A Martienssen; German Martinez; Claudia Köhler
Journal:  Plant Cell       Date:  2020-01-27       Impact factor: 11.277

5.  Arabidopsis RNA Polymerase IV generates 21-22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes.

Authors:  Kaushik Panda; Andrea D McCue; R Keith Slotkin
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2020-02-10       Impact factor: 6.237

Review 6.  The role of environmental exposures and the epigenome in health and disease.

Authors:  Bambarendage P U Perera; Christopher Faulk; Laurie K Svoboda; Jaclyn M Goodrich; Dana C Dolinoy
Journal:  Environ Mol Mutagen       Date:  2019-06-20       Impact factor: 3.216

7.  A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog, Platyplectrum ornatum.

Authors:  Sangeet Lamichhaney; Renee Catullo; J Scott Keogh; Simon Clulow; Scott V Edwards; Tariq Ezaz
Journal:  Proc Natl Acad Sci U S A       Date:  2021-03-16       Impact factor: 11.205

8.  Quantitative sequence characterization for repetitive DNA content in the supernumerary chromosome of the migratory locust.

Authors:  Francisco J Ruiz-Ruano; Josefa Cabrero; María Dolores López-León; Antonio Sánchez; Juan Pedro M Camacho
Journal:  Chromosoma       Date:  2017-09-04       Impact factor: 4.316

9.  Human ADAR1 Prevents Endogenous RNA from Triggering Translational Shutdown.

Authors:  Hachung Chung; Jorg J A Calis; Xianfang Wu; Tony Sun; Yingpu Yu; Stephanie L Sarbanes; Viet Loan Dao Thi; Abigail R Shilvock; H-Heinrich Hoffmann; Brad R Rosenberg; Charles M Rice
Journal:  Cell       Date:  2018-01-25       Impact factor: 41.582

10.  Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of nonclassic domestication.

Authors:  Hideo Matsumura; Min-Chien Hsiao; Ya-Ping Lin; Atsushi Toyoda; Naoki Taniai; Kazuhiko Tarora; Naoya Urasaki; Shashi S Anand; Narinder P S Dhillon; Roland Schafleitner; Cheng-Ruei Lee
Journal:  Proc Natl Acad Sci U S A       Date:  2020-05-27       Impact factor: 11.205
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